BCFTOOLS CALL
Call variants with bcftools call.
URL: http://www.htslib.org/doc/bcftools.html#call
Example
This wrapper can be used in the following way:
rule bcftools_call:
input:
pileup="{sample}.pileup.bcf",
output:
calls="{sample}.calls.bcf",
params:
uncompressed_bcf=False,
caller="-m", # valid options include -c/--consensus-caller or -m/--multiallelic-caller
extra="--ploidy 1 --prior 0.001",
log:
"logs/bcftools_call/{sample}.log",
wrapper:
"v5.7.0/bio/bcftools/call"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Notes
The uncompressed_bcf param allows to specify that a BCF output should be uncompressed (ignored otherwise).
The extra param allows for additional program arguments (not –threads, -o/–output, or -O/–output-type).
Software dependencies
bcftools=1.21
snakemake-wrapper-utils=0.6.2
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
class CallerOptionError(Exception):
pass
valid_caller_opts = {"-c", "--consensus-caller", "-m", "--multiallelic-caller"}
caller_opt = snakemake.params.get("caller", "")
if caller_opt.strip() not in valid_caller_opts:
raise CallerOptionError(
"bcftools call expects either -m/--multiallelic-caller or "
"-c/--consensus-caller as caller option."
)
shell(
"bcftools call"
" {bcftools_opts}"
" {caller_opt}"
" {extra}"
" {snakemake.input[0]}"
" {log}"
)